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Molecular variability of Apple chlorotic leaf spot virus in Shaanxi, China

Phytoparasitica volume 42, pages 445–454 (2014)Cite this article

Abstract

Apple chlorotic leaf spot virus (ACLSV) is one of the latent viruses that occur in apple orchards worldwide but usually without visible symptoms. In 2010–2012, a total of 550 apple leaf samples from 12 different major apple-producing areas in Shaanxi, China, were tested by serological assay for ACLSV; the results revealed an infection level of 51.5 %. Because of the known variability in the putative amino acid sequences of the coat protein (CP), and thus the potential for non-detection by serological assay, the molecular variability of isolates of ACLSV collected in Shaanxi was analyzed using PCR and compared with isolates from the rest of the world. Sequences of 504 nt corresponding to 87 % of the CP gene of 12 isolates were acquired by RT-PCR and deposited in GenBank with the accession numbers KF134387–KF134298. Comparisons of the partial CP gene sequences of these 12 isolates as well as isolates previously reported in the world revealed the pairwise identities ranging from 68.9–99.8 % and 73.8–100 % at the nucleotide and amino acid level, respectively. Phylogenetic analysis based on these nucleotide sequences showed that the 72 isolates deposited in GenBank fell into three groups (P205, B6 and Ta Tao 5 Group). Our 12 ACLSV isolates were separated into the P205 and B6 groups, respectively. Multiple alignment analysis of the amino acid sequences of CP revealed that there was a combination of six amino acids at positions 40, 59, 75, 86, 130 and 184 in isolates from each group that could be used to distinguish among the three groups. Two recombination events were identified from all isolates by recombination analysis, and three ACLSV isolates collected in this study participated in these two events. Our results show that molecular variation was present in isolates of ACLSV collected in Shaanxi province and this may reflect introductions of the virus associated with different sources of germplasm.

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References

  • Al Rwahnih, M., Turturo, C., Minafra, A., Saldarelli, P., Myrta, A., Pallás, V., et al. (2004). Molecular variability of Apple chlorotic leaf spot virus in different hosts and geographical regions. Journal of Plant Pathology, 86, 117–122.

    Google Scholar 

  • Asif, M., Trivedi, P., Solomos, T., & Tucker, M. (2006). Isolation of high-quality RNA from apple (Malus domestica) fruit. Journal of Agricultural and Food Chemistry, 54, 5227–5229.

    CAS  PubMed  Article  Google Scholar 

  • Candresse, T., Lanneau, M., Revers, F., Grasseau, N., Macquaire, G., German, S., et al. (1995). An immunocapture PCR assay adapted to the detection and the analysis of the molecular variability of apple chlorotic leaf spot virus. Acta Horticulturae, 386, 136–147.

    CAS  Google Scholar 

  • Carstens, E. (2010). Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2009). Archives of Virology, 155, 133–146.

    CAS  PubMed  Article  Google Scholar 

  • Corpet, F. (1988). Multiple sequence alignment with hierarchical clustering. Nucleic Acids Research, 16, 10881–10890.

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Desvignes, J., & Boyé, R. (1989). Different diseases caused by the chlorotic leaf spot virus on the fruit trees. Acta Horticulturae, 235, 31–38.

    Google Scholar 

  • Desvignes, J. C., Boyé, R., Cornaggia, D., Grasseau, N., Hurtt, S., & Waterworth, H. (1999). Virus diseases of fruit trees. (pp. 239–252). Paris, France: Centre Technique Interprofessionnel des Fruits et Légumes (CTIFL).

  • Dhir, S., Zaidi, A. A., & Hallan, V. (2013). Molecular characterization and recombination analysis of the complete genome of Apple chlorotic leaf spot virus. Journal of Phytopathology, 161, 704–712.

    CAS  Article  Google Scholar 

  • Drummon, A., Oliver, G., & Rambaut, A. (2003). Inference of viral evolutionary rates from molecular sequences. Advances in Parasitology, 54, 331–358.

    Article  Google Scholar 

  • Dunez, J., Marenaud, C., Delbos, R., & Lansac, M. (1972). Variability of symptoms induced by the apple chlorotic leaf spot (CLSV) – a type of CLSV probably responsible for bark split disease of prune trees. Plant Disease Reporter, 56, 293–295.

    Google Scholar 

  • Fu, Y.-X., & Li, W.-H. (1993). Statistical tests of neutrality of mutations. Genetics, 133, 693–709.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Gagarinova, A. G., Babu, M., Strömvik, M. V., & Wang, A. (2008). Recombination analysis of Soybean mosaic virus sequences reveals evidence of RNA recombination between distinct pathotypes. Virology Journal, 5, 143.

    PubMed Central  PubMed  Article  Google Scholar 

  • García-Arenal, F., Fraile, A., & Malpica, J. M. (2001). Variability and genetic structure of plant virus populations. Annual Review of Phytopathology, 39, 157–186.

    PubMed  Article  Google Scholar 

  • German, S., Candresse, T., Lanneau, M., Huet, J., Pernollet, J., & Dunez, J. (1990). Nucleotide sequence and genomic organization of apple chlorotic leaf spot closterovirus. Virology, 179, 104–112.

    CAS  PubMed  Article  Google Scholar 

  • German-Retana, S., Bergey, B., Delbos, R., Candresse, T., & Dunez, J. (1997). Complete nucleotide sequence of the genome of a severe cherry isolate of apple chlorotic leaf spot trichovirus (ACLSV). Archives of Virology, 142, 833–841.

    CAS  PubMed  Article  Google Scholar 

  • Jelkmann, W., & Kunze, L. (1995). Plum pseudopox in German plum after infection with an isolate of apple chlorotic leaf spot virus causing plum line pattern. Acta Horticulturae, 386, 122–125.

    Google Scholar 

  • Karan, M., Harding, R. M., & Dale, J. L. (1994). Evidence for two groups of banana bunchy top virus isolates. Journal of General Virology, 75, 3541–3546.

    CAS  PubMed  Article  Google Scholar 

  • Li, R., Mock, R., Huang, Q., Abad, J., Hartung, J., & Kinard, G. (2008). A reliable and inexpensive method of nucleic acid extraction for the PCR-based detection of diverse plant pathogens. Journal of Virological Methods, 154, 48–55.

    CAS  PubMed  Article  Google Scholar 

  • Librado, P., & Rozas, J. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451–1452.

    CAS  PubMed  Article  Google Scholar 

  • Liu, N., Niu, J., & Zhao, Y. (2012). Complete genomic sequence analyses of Apple stem pitting virus isolates from China. Virus Genes, 44, 124–130.

    CAS  PubMed  Article  Google Scholar 

  • Liu, P., Zhang, L., Zhang, H., Jiao, H., & Wu, Y. (2013). Detection and molecular variability of Apple stem grooving virus in Shaanxi, China. Journal of Phytopathology, 161, 445–449.

    CAS  Article  Google Scholar 

  • Marini, D., Gibson, P., & Scott, S. (2008). The complete nucleotide sequence of an isolate of Apple chlorotic leaf spot virus from peach (Prunus persica (L.) Batch). Archives of Virology, 153, 1003–1005.

    CAS  PubMed  Article  Google Scholar 

  • Martelli, G., Candresse, T., & Namba, S. (1994). Trichovirus, a new genus of plant viruses. Archives of Virology, 134, 451–455.

    CAS  PubMed  Article  Google Scholar 

  • Martelli, G. P., Adams, M. J., Kreuze, J. F., & Dolja, V. V. (2007). Family Flexiviridae: a case study in virion and genome plasticity. Annual Review of Phytopathology, 45, 73–100.

    CAS  PubMed  Article  Google Scholar 

  • Martin, D., & Rybicki, E. (2000). RDP: detection of recombination amongst aligned sequences. Bioinformatics, 16, 562–563.

    CAS  PubMed  Article  Google Scholar 

  • Martin, D. P., Lemey, P., Lott, M., Moulton, V., Posada, D., & Lefeuvre, P. (2010). RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics, 26, 2462–2463.

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Menzel, W., Jelkmann, W., & Maiss, E. (2002). Detection of four apple viruses by multiplex RT-PCR assays with coamplification of plant mRNA as internal control. Journal of Virological Methods, 99, 81–92.

    CAS  PubMed  Article  Google Scholar 

  • Muhire, B., Martin, D. P., Brown, J. K., Navas-Castillo, J., Moriones, E., Zerbini, F. M., et al. (2013). A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Archives of Virology, 1–14.

  • Nemeth, M. (1986). Virus, mycoplasma and rickettsia diseases of fruit trees. Budapest, Hungary: Akademiai Kiado

  • Niu, F., Pan, S., Wu, Z., Jiang, D., & Li, S. (2012). Complete nucleotide sequences of the genomes of two isolates of apple chlorotic leaf spot virus from peach (Prunus persica) in China. Archives of Virology, 157, 783–786.

    CAS  PubMed  Article  Google Scholar 

  • Pasquini, G., Faggioli, F., Pilotti, M., Lumia, V., & Barba, M. (1998). Characterization of Apple chlorotic leaf spot virus isolates from Italy. Acta Horticulturae, 472, 195–199.

    CAS  Google Scholar 

  • Peña-Iglesias, A., & Ayuso Gonzalez, P. (1975). Preliminary identification of the viruses producing Spanish apricot pseudopox (viruela) and apricot mosaic diseases. Acta Horticulturae, 44, 255–268.

    Google Scholar 

  • Ragozzino, A., & Pugliano, G. (1974). La butteratura delle albicocche. Indagini preliminari sulla eziologia. Rivista dell’Ortoflorofrutticoltura Italiana, 58, 136–145.

    Google Scholar 

  • Revers, F., Le Gall, O., Candresse, T., Le Romancer, M., & Dunez, J. (1996). Frequent occurrence of recombinant potyvirus isolates. Journal of General Virology, 77, 1953–1965.

    CAS  PubMed  Article  Google Scholar 

  • Rico, P., Ivars, P., Elena, S. F., & Hernández, C. (2006). Insights into the selective pressures restricting Pelargonium flower break virus genome variability: evidence for host adaptation. Journal of Virology, 80, 8124–8132.

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Sato, K., Yoshikawa, N., & Takahashi, T. (1993). Complete nucleotide sequence of the genome of an apple isolate of apple chlorotic leaf spot virus. Journal of General Virology, 74, 1927.

    CAS  PubMed  Article  Google Scholar 

  • Schroeder, M., & Weidemann, H. L. (1989). Simplified application of return gel electrophoresis for the routine detection of potato spindle tuber viroid. EPPO Bulletin, 19, 661–665.

    Article  Google Scholar 

  • Seo, J.-K., Ohshima, K., Lee, H.-G., So, M., Choi, H.-S., Lee, S.-H., et al. (2009). Molecular variability and genetic structure of the population of Soybean mosaic virus based on the analysis of complete genome sequences. Virology, 393, 91–103.

    CAS  PubMed  Article  Google Scholar 

  • Tajima, F. (1983). Evolutionary relationship of DNA sequences in finite populations. Genetics, 105, 437–460.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585–595.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731–2739.

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Varsani, A., Shepherd, D. N., Monjane, A. L., Owor, B. E., Erdmann, J. B., Rybicki, E. P., et al. (2008). Recombination, decreased host specificity and increased mobility may have driven the emergence of Maize streak virus as an agricultural pathogen. Journal of General Virology, 89, 2063–2074.

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Wang, G., Hong, N., Zhang, Z., Hu, S., & Dong, Y. (1994). Identification of virus species in pears cultivated in northern China. China Fruits, 2, 1–4.

    Google Scholar 

  • Watterson, G. (1975). On the number of segregating sites in genetical models without recombination. Theoretical Population Biology, 7, 256–276.

    CAS  PubMed  Article  Google Scholar 

  • Yaegashi, H., Isogai, M., Tajima, H., Sano, T., & Yoshikawa, N. (2007). Combinations of two amino acids (Ala40 and Phe75 or Ser40 and Tyr75) in the coat protein of Apple chlorotic leaf spot virus are crucial for infectivity. Journal of General Virology, 88, 2611–2618.

    CAS  PubMed  Article  Google Scholar 

  • Yanase, H. (1974). Studies on apple latent viruses in Japan: The association of apple top-working disease with apple latent viruses. Bulletin of the Fruit Tree Research Station. Series C. Morioka. 47-109

  • Yang, Z., & Bielawski, J. P. (2000). Statistical methods for detecting molecular adaptation. Trends in Ecology & Evolution, 15, 496–503.

    Article  Google Scholar 

  • Yoshikawa, N., & Takahashi, T. (1988). Properties of RNAs and proteins of apple stem grooving and apple chlorotic leaf spot viruses. Journal of General Virology, 69, 241–245.

    CAS  Article  Google Scholar 

  • Zhang, X., Zhu, H., & Zhang, H. (2005). Present situation and developing thought of apple industry in Shaanxi. Journal of Northwest University(Philosophy and Social Sciences Edition), 35, 36–41.

    Google Scholar 

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Acknowledgments

This work was supported by the 111 project (Grant No. B07049) and the National High-tech R&D Program of China (2012AA101504). The authors are grateful to fruit growers for their cooperation during the surveys and to Tao Ye for careful reading of the manuscript.

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Authors and Affiliations

  1. State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China

    Ping Liu, Zhengnan Li, Shuang Song & Yunfeng Wu

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  1. Ping Liu
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  2. Zhengnan Li
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Correspondence to Yunfeng Wu.

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Liu, P., Li, Z., Song, S. et al. Molecular variability of Apple chlorotic leaf spot virus in Shaanxi, China. Phytoparasitica 42, 445–454 (2014). https://doi.org/10.1007/s12600-013-0381-2

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Keywords

  • Coat protein gene
  • Multiple alignment
  • Phylogenetic analysis